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. 2024 Dec 12;13(12):1096.
doi: 10.3390/pathogens13121096.

Characterization and Genomics of Pectinolytic Bacteria Isolated from Soft Rot Symptomatic Produce

Kyla Radke  1 , Brandon Rivers  1 , Mya Simpkins  1 , Jacob Hardy  1 , Jeffrey K Schachterle  1
Affiliations

Characterization and Genomics of Pectinolytic Bacteria Isolated from Soft Rot Symptomatic Produce

Kyla Radke et al. Pathogens. .

Abstract

Bacterial soft rot causes major crop losses annually and can be caused by several species from multiple genera. These bacteria have a broad host range and often infect produce through contact with soil. The main genera causing bacterial soft rot are Pectobacterium and Dickeya, both of which have widespread geographical distribution. Because of many recent renaming and reclassifications of bacteria causing soft rot, identification and characterization of the causative agents can be challenging. In this work, we surveyed commercially available produce exhibiting typical soft rot symptoms, isolating pectinolytic bacteria and characterizing them genetically and phenotypically. We found that in our sampling, many samples were from the genus Pectobacterium; however, other genera were also capable of eliciting symptoms in potatoes, including an isolate from the genus Chryseobacterium. Genomic analyses revealed that many of the Pectobacterium isolates collected share prophages not found in other soft rot species, suggesting a potential role for these prophages in the evolution or fitness of these isolates. Our Chryseobacterium isolate was most similar to C. scophthalmum, a fish pathogen, suggesting that this isolate may be a crossover pathogen.

Keywords: Chryseobacterium; Pectobacterium; Pseudomonas; pectinolytic; soft rot.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Virulence of isolates as measured by area of lesion on inoculated potato slices (A) and biofilm formation in 96-well plates following static growth for 48 h (B).
Figure 2
Figure 2
Average nucleotide identity of Pectobacterium isolates represented as a heatmap. (A) ANI across all type strains of Pectobacterium and Dickeya species in RefSeq database (n = 41 genomes). (B) ANI across all genomes entered in RefSeq database as P. carotovorum (n = 103 genomes). (C) ANI across all genomes entered in RefSeq database as P. versatile (n = 105 genomes).
Figure 3
Figure 3
Average nucleotide identity of Pseudomonas isolates from our survey and type strains of all species in the RefSeq database (n = 375 genomes).
Figure 4
Figure 4
Average nucleotide identity of the Chryseobacterium isolate and all type strains from Chryseobacterium species in the RefSeq database (n = 118 genomes).
Figure 5
Figure 5
Whole genome alignments of P. carotovorum isolates M3, M4a, M8a, and M8b. Alignment and visualization generated by Mauve.
Figure 6
Figure 6
Prophage dendrogram. Newick tree generated by ANIclustermap using sequences of prophages predicted by Phastest in newly sequenced Pectobacterium genomes. Representation rendered by ETEToolkit.
See this image and copyright information in PMC

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